In 1125, Matilda married Stephen of Blois, Count of Mortain, who possessed a large honour in England. When Matilda's father abdicated and retired to a monastery the same year, this was joined with Boulogne and the similarly large English honour Matilda inherited. On Eustace III's death, Matilda and her husband became joint rulers of Boulogne. Two children, a son and a daughter, were born to the countess and count of Boulogne during the reign of King Henry I, who had granted them a residence in London.[1] The son was named Baldwin, after Matilda's uncle, King Baldwin I of Jerusalem.[1] The daughter was named Matilda. Baldwin died in early childhood and the young Matilda is thought to have died during childhood too, although she lived long enough to be espoused to Waleran de Meulan, Earl of Worcester.[1]

On the death of Henry I of England in 1135, Stephen rushed to England, taking advantage of Boulogne's control of the closest seaports, and was crowned king, beating his rival, the Empress Matilda. Matilda of Boulogne was heavily pregnant at that time and crossed the Channel after giving birth to a son, Eustace, who would one day succeed her as count of Boulogne. Matilda was crowned queen at Easter - 22 March 1136.[1]

In the civil war that followed, known as the Anarchy, Matilda proved to be her husband's strongest supporter. When England was invaded in 1138, she called troops from Boulogne and its ally Flanders, and besieged Dover Castle with success and then went north to Durham, where she made a treaty with David I of Scotland in 1139.[4]

After Stephen was captured at the Battle of Lincoln in 1141, she rallied the king's partisans, and raised an army with the help of William of Ypres. While the Empress Matilda waited in London to prepare her coronation, Matilda and Stephen's brother Henry of Blois had her chased out of the city. The Empress Matilda went on to besiege Henry of Blois at Winchester. Matilda of Boulogne then commanded her army to attack the besiegers. There was a rout in which the Empress's half-brother, Robert of Gloucester, was captured. The two Matildas then agreed to exchange prisoners and Stephen ruled as king again.[5]